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Firstly, in this paper a theoretical scheme on the mechanisms of the analogical thinking in science education is summarised. Secondly, the degree of understanding reached by a group of students about the analogies used in class on the molecular model is analyzed. Finally, the relationship between analogical thinking and the students’ mental models about the nature of the matter is studied. The collected data indicate a moderate but acceptable final level of understanding of the analogies used, as well the existence of a narrow relationship between the understanding analogies and the construction of a model for the matter.